Bonds are too long after simulation

From: Anthony Rey (
Date: Wed Sep 07 2011 - 10:32:11 CDT


Thanks for accepting my email address on the mailing list. I have been
using NAMD for a while now but can't figure out what's going on with
the simulation.
I am basically doing the same simulation as the Ubiquitin unfolding
tutorial except I use it for a protein structure that I solved by NMR.
I created the psf from the pdb and made sure that I didn't get any
error messages (except from the N-terminal and C-terminal residues :
poorly guessed residues).

Then, I ran a script to put my protein into a water sphere. The output
files look normal (both psf and pdb). I ran the simulation (5000
minimisation steps + 50 000 steps for the simulation), put the right
diameter and center of the sphere for the spherical boundary conditions
into the configuration file.

When I look at the output, the minimization was long enough and the
system looks quite stable at the end of the simulation. However, I do
get some abnormalities when I look at the structure into VMD: the bonds
get bigger during the simulation.

The bonds are bigger but they are not huge. From what I've seen in the
forum, a lot of people have similar issues except that they got huge
bonds which I don't. I don't have long bonds at the beginning of the
simulation, and I don't have any atoms that have {0.00 0.00 0.00}
coordinates in the pdb either. The bonds just increase in length during
the experiment, and the longer the experiment, the longer the bonds....

Is is normal that the bond length increases with the simulation? Is
there a way to fix this?

I would really appreciate your help as I have no idea how to fix this.
Please let me know if you need further details about the simulation.

Best regards,


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